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- EMDB-43014: Phosphorylated, ATP-bound, inhibitor 172-bound E1371Q human cysti... -

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Basic information

Entry
Database: EMDB / ID: EMD-43014
TitlePhosphorylated, ATP-bound, inhibitor 172-bound E1371Q human cystic fibrosis transmembrane conductance regulator
Map data
Sample
  • Complex: E1371Q-CFTR
    • Protein or peptide: Cystic fibrosis transmembrane conductance regulator
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: CHOLESTEROL
  • Ligand: 4-[(Z)-{(3M)-4-oxo-2-sulfanylidene-3-[3-(trifluoromethyl)phenyl]-1,3-thiazolidin-5-ylidene}methyl]benzoic acid
Keywordscystic fibrosis / chloride channel / hydrolysis-deficient mutant / MEMBRANE PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of voltage-gated chloride channel activity / positive regulation of cyclic nucleotide-gated ion channel activity / Sec61 translocon complex binding / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / positive regulation of enamel mineralization / transepithelial water transport / RHO GTPases regulate CFTR trafficking / intracellular pH elevation / amelogenesis ...positive regulation of voltage-gated chloride channel activity / positive regulation of cyclic nucleotide-gated ion channel activity / Sec61 translocon complex binding / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / positive regulation of enamel mineralization / transepithelial water transport / RHO GTPases regulate CFTR trafficking / intracellular pH elevation / amelogenesis / chloride channel inhibitor activity / ATPase-coupled inorganic anion transmembrane transporter activity / Golgi-associated vesicle membrane / multicellular organismal-level water homeostasis / cholesterol transport / membrane hyperpolarization / vesicle docking involved in exocytosis / bicarbonate transport / bicarbonate transmembrane transporter activity / chloride channel regulator activity / chloride transmembrane transporter activity / sperm capacitation / chloride channel activity / cholesterol biosynthetic process / RHOQ GTPase cycle / positive regulation of exocytosis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / chloride channel complex / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / cellular response to cAMP / cellular response to forskolin / chloride transmembrane transport / response to endoplasmic reticulum stress / isomerase activity / clathrin-coated endocytic vesicle membrane / establishment of localization in cell / PDZ domain binding / Defective CFTR causes cystic fibrosis / Late endosomal microautophagy / ABC-family proteins mediated transport / recycling endosome / transmembrane transport / Aggrephagy / Chaperone Mediated Autophagy / recycling endosome membrane / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / early endosome membrane / protein-folding chaperone binding / endosome membrane / early endosome / Ub-specific processing proteases / apical plasma membrane / lysosomal membrane / endoplasmic reticulum membrane / enzyme binding / cell surface / ATP hydrolysis activity / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / CFTR regulator domain / Cystic fibrosis TM conductance regulator (CFTR), regulator domain / Cystic fibrosis transmembrane conductance regulator / : / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site ...: / CFTR regulator domain / Cystic fibrosis TM conductance regulator (CFTR), regulator domain / Cystic fibrosis transmembrane conductance regulator / : / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Cystic fibrosis transmembrane conductance regulator
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGao X / Hwang T
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
Cystic Fibrosis Foundation United States
CitationJournal: Nat Commun / Year: 2024
Title: Allosteric inhibition of CFTR gating by CFTRinh-172 binding in the pore.
Authors: Xiaolong Gao / Han-I Yeh / Zhengrong Yang / Chen Fan / Fan Jiang / Rebecca J Howard / Erik Lindahl / John C Kappes / Tzyh-Chang Hwang /
Abstract: Loss-of-function mutations of the CFTR gene cause the life-shortening genetic disease cystic fibrosis (CF), whereas overactivity of CFTR may lead to secretory diarrhea and polycystic kidney disease. ...Loss-of-function mutations of the CFTR gene cause the life-shortening genetic disease cystic fibrosis (CF), whereas overactivity of CFTR may lead to secretory diarrhea and polycystic kidney disease. While effective drugs targeting the CFTR protein have been developed for the treatment of CF, little progress has been made for diseases caused by hyper-activated CFTR. Here, we solve the cryo-EM structure of CFTR in complex with CFTRinh-172 (Inh-172), a CFTR gating inhibitor with promising potency and efficacy. We find that Inh-172 binds inside the pore of CFTR, interacting with amino acid residues from transmembrane segments (TMs) 1, 6, 8, 9, and 12 through mostly hydrophobic interactions and a salt bridge. Substitution of these residues lowers the apparent affinity of Inh-172. The inhibitor-bound structure reveals re-orientations of the extracellular segment of TMs 1, 8, and 12, supporting an allosteric modulation mechanism involving post-binding conformational changes. This allosteric inhibitory mechanism readily explains our observations that pig CFTR, which preserves all the amino acid residues involved in Inh-172 binding, exhibits a much-reduced sensitivity to Inh-172 and that the apparent affinity of Inh-172 is altered by the CF drug ivacaftor (i.e., VX-770) which enhances CFTR's activity through binding to a site also comprising TM8.
History
DepositionDec 4, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43014.png

Downloads & links

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Map

FileDownload / File: emd_43014.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.069 Å
Density
Contour LevelBy AUTHOR: 0.0088
Minimum - Maximum-0.09240413 - 0.10628135
Average (Standard dev.)0.0000123268655 (±0.0021272262)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 277.94 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_43014_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43014_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : E1371Q-CFTR

EntireName: E1371Q-CFTR
Components
  • Complex: E1371Q-CFTR
    • Protein or peptide: Cystic fibrosis transmembrane conductance regulator
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: CHOLESTEROL
  • Ligand: 4-[(Z)-{(3M)-4-oxo-2-sulfanylidene-3-[3-(trifluoromethyl)phenyl]-1,3-thiazolidin-5-ylidene}methyl]benzoic acid

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Supramolecule #1: E1371Q-CFTR

SupramoleculeName: E1371Q-CFTR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cystic fibrosis transmembrane conductance regulator

MacromoleculeName: Cystic fibrosis transmembrane conductance regulator / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: channel-conductance-controlling ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 163.494078 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: RSPLEKASVV SKLFFSWTRP ILRKGYRQRL ELSDIYQIPS VDSADNLSEK LEREWDRELA SKKNPKLINA LRRCFFWRFM FYGIFLYLG EVTKAVQPLL LGRIIASYDP DNKEERSIAI YLGIGLCLLF IVRTLLLHPA IFGLHHIGMQ MRIAMFSLIY K KTLKLSSR ...String:
RSPLEKASVV SKLFFSWTRP ILRKGYRQRL ELSDIYQIPS VDSADNLSEK LEREWDRELA SKKNPKLINA LRRCFFWRFM FYGIFLYLG EVTKAVQPLL LGRIIASYDP DNKEERSIAI YLGIGLCLLF IVRTLLLHPA IFGLHHIGMQ MRIAMFSLIY K KTLKLSSR VLDKISIGQL VSLLSNNLNK FDEGLALAHF VWIAPLQVAL LMGLIWELLQ ASAFCGLGFL IVLALFQAGL GR MMMKYRD QRAGKISERL VITSEMIENI QSVKAYCWEE AMEKMIENLR QTELKLTRKA AYVRYFNSSA FFFSGFFVVF LSV LPYALI KGIILRKIFT TISFCIVLRM AVTRQFPWAV QTWYDSLGAI NKIQDFLQKQ EYKTLEYNLT TTEVVMENVT AFWE EGFGE LFEKAKQNNN NRKTSNGDDS LFFSNFSLLG TPVLKDINFK IERGQLLAVA GSTGAGKTSL LMVIMGELEP SEGKI KHSG RISFCPQFPW IMPGTIKENI IFGVSYDEYR YRSVIKACQL EEDISKFPEK DNTVLGEGGI TLSGGQRAKI SLARAV YKD ADLYLLDSPF GYLDVLTEKE IFESCVCKLM ANKTRILVTS KMEHLKKADK ILILHEGSSY FYGTFSELQN LQPDFSS KL MGCDSFDQFS AERRNSILTE TLHRFSLEGD APVSWTETKK QSFKQTGEFG EKRKNSILNP INSIRKFSIV QKTPLQMN G IEEDSDEPLE RRLSLVPDSE QGEAILPRIS VISTGPTLQA RRRQSVLNLM THSVNQGQNI HRKTTASTRK VSLAPQANL TELDIYSRRL SQETGLEISE EINEEDLKEC FFDDMESIPA VTTWNTYLRY ITVHKSLIFV LIWCLVIFLA EVAASLVVLW LLGNTPLQD KGNSTHSRNN SYAVIITSTS SYYVFYIYVG VADTLLAMGF FRGLPLVHTL ITVSKILHHK MLHSVLQAPM S TLNTLKAG GILNRFSKDI AILDDLLPLT IFDFIQLLLI VIGAIAVVAV LQPYIFVATV PVIVAFIMLR AYFLQTSQQL KQ LESEGRS PIFTHLVTSL KGLWTLRAFG RQPYFETLFH KALNLHTANW FLYLSTLRWF QMRIEMIFVI FFIAVTFISI LTT GEGEGR VGIILTLAMN IMSTLQWAVN SSIDVDSLMR SVSRVFKFID MPTEGKPTKS TKPYKNGQLS KVMIIENSHV KKDD IWPSG GQMTVKDLTA KYTEGGNAIL ENISFSISPG QRVGLLGRTG SGKSTLLSAF LRLLNTEGEI QIDGVSWDSI TLQQW RKAF GVIPQKVFIF SGTFRKNLDP YEQWSDQEIW KVADEVGLRS VIEQFPGKLD FVLVDGGCVL SHGHKQLMCL ARSVLS KAK ILLLDQPSAH LDPVTYQIIR RTLKQAFADC TVILCEHRIE AMLECQQFLV IEENKVRQYD SIQKLLNERS LFRQA

UniProtKB: Cystic fibrosis transmembrane conductance regulator

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #4: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 4 / Number of copies: 5 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #5: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 5 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #6: 4-[(Z)-{(3M)-4-oxo-2-sulfanylidene-3-[3-(trifluoromethyl)phenyl]-...

MacromoleculeName: 4-[(Z)-{(3M)-4-oxo-2-sulfanylidene-3-[3-(trifluoromethyl)phenyl]-1,3-thiazolidin-5-ylidene}methyl]benzoic acid
type: ligand / ID: 6 / Number of copies: 1 / Formula: WG5
Molecular weightTheoretical: 409.402 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.31475 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 140837
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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